Ryan Anthony W. (ed.) Celiac Disease: Methods and Protocols

Humana Press, 2015. — 249 p. — (Methods in Molecular Biology 1326) — ISBN: 978-1-4939-2838-5This volume provides detailed molecular analysis of the associated pathways and cell types involved in Celiac Disease, and embraces new technologies such as next generation sequencing. The book is divided into three parts: Part I gives a background overview with a number of reviews to describe the history and nature of the disease, its diagnosis, the role of animal models, and study designs for investigating genetic susceptibility. Part II describes molecular techniques, including tissue culture, isolation and cloning of relevant cell types, high content analysis of biopsies, and HLA genotyping. The final part of the book begins with an outline of scripting for data management, focusing on tools that are freely available to researchers who wish to explore them. It also describes analysis pipelines for bioinformatics prediction of antigenicity, quality control and analysis of GWAS data, and transcriptome analysis by next generation sequencing. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Authoritative and thorough, Celiac Disease: Methods and Protocols brings together novel and more traditional methods in molecular biology and immunology, in order to provide a tool-kit for all stages for Celiac Disease research—from the practicalities of identifying, obtaining, stabilizing and maintaining high quality samples, to molecular analysis and bioinformatics.Background
Celiac Disease: Background and Historical Context
Celiac Disease: Diagnosis
Generating Transgenic Mouse Models for Studying Celiac Disease
Study Designs for Exploring the Non-HLA Genetics in Celiac Disease
Laboratory Protocols
Twenty-Four Hour Ex Vivo Culture of Celiac Duodenal Biopsies
Isolation and Cloning of Gluten-Specific T Cells in Celiac Disease
Flow Cytometric Analysis of Human Small Intestinal Lymphoid Cells
Adaptation of a Cell-Based High Content Screening System for the In-Depth Analysis of Celiac Biopsy Tissue
HLA Genotyping: Methods for the Identification of the HLA-DQ2,-DQ8 Heterodimers Implicated in Celiac Disease (CD) Susceptibility
Detecting Allelic Expression Imbalance at Candidate Genes Using 5′ Exonuclease Genotyping Technology
Gene Expression Profiling of Celiac Biopsies and Peripheral Blood Monocytes Using Taqman Assays
Cloning Gene Variants and Reporter Assays
Epigenetic Methodologies for the Study of Celiac Disease
Candidate Gene Knockdown in Celiac Disease
Bioinformatic
Perl One-Liners: Bridging the Gap Between Large Data Sets and Analysis Tools
Bioinformatic Analysis of Antigenic Proteins in Celiac Disease
Quality Control Procedures for High-Throughput Genetic Association Studies
Quality Control and Analysis of NGS RNA Sequencing Data